Please edit MetaboNews spotlight article on nmrML

[D Schober]

Dear all,

 As requested during our last nmrML hangout, I have drafted a backbone for a MetaboNews spotlight article on nmrML.
Please have a go, and edit/refine the current GoogleDoc at
https://docs.google.com/document/d/1R3e0ytPcNLmTx3M0hkwRQj2M4IJ00-KU2vnSjz8U6-I/edit#

Deadline is Nov 15th (strict!), so not too much time left.

Best regards,
    Daniel Schober

-- 

Dr. Daniel Schober
Leibniz Institute of Plant Biochemistry, http://www.IPB-Halle.de
Dept. for Stress and Developmental Biology Bioinformatics & Mass Spectrometry
Weinberg 3 Tel. +49 (0) 345 5582 - 1476
06120 Halle

[Reza Salek]

Please check my feedbacks. I think there are too many figures the reset is minor corrections and look good. Need more justification to start with. Why we need it?

Daniel can you send me the short info for the format?

Best wishes,

Reza

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[Antonio Rosato]

It reads well, but way too many figures. I would remove Figures 3-6 altogether. 

Perhaps a short end paragraph with a hint on future developments is in order? It'd also be nice to make a mention of MetaboLights somewhere

Best regards

Antonio

[Michael Wilson]

I have added some suggested edits, that respond to some of the other peoples comments.

Mike

[Ebbels, Timothy M D]

I also added a few comments. My main feeling is that it is a bit long for metabonews. Perhaps it’s just the large number of figures – could some of these be dropped?

Tim

[Steffen Neumann]

Dear all, 

I am currently writing up a generic data standards review/tutorial 
from the COSMOS point of view, where some of you are already co-authors.
The review includes a lot of high level discussion on how and why to do data standards. 
It covers ISAtab concepts, but also mzML as raw data standard.

To mention the existence of nmrML, I have used our last MetaboNews article and condensed that 
even further into the following paragraph for this data standards tutorial. Please check 
that this is OK for you or contact me if there is something missing.

Yours,
Steffen


NMR raw data standards
======================
For NMR data, the The Metabolomics Innovation Centre (TMIC) in Canada
and the COordination of Standards in MetabOlomicS (COSMOS) consortium in
Europe as well as other interested groups have developed the XML based,
vendor-neutral open exchange and data storage format nmrML, which builds
on earlier efforts, and reporting requirements described by Rubtsov et
al. The format has also heavily borrowed ideas from the HUPO-PSI mzML
standard, including an XML schema that defines the structure of an nmrML
file and a supporting controlled vocabulary (nmrCV), which allows the
reuse of nmrCV terms in other formats and tools. The development of
nmrML takes place on www.nmrml.org, where the specification documents,
examples files, and converters can be found. Java, Python, R and Matlab
parsers have been developed to convert raw vendor formats to nmrML.
Validator tools are available to check the generated nmrML files on
quality aspects like completeness and correct semantics. We would like
to make developers of NMR data analysis software aware of this effort,
to contact us and implement access to this open format. Likewise, users
should start considering to submit their 1D NMR data to metabolomics
repositories like MetaboLights in the nmrML format.